That's odd, but understandable. Thunderbird considers the Templates folder to be a "system" folder. Once it is created, it can be a chore to remove it. Check your settings in Tools | Account Settings | account | Copies & Folders for each account. Are you referencing the Templates folder in each account? If so, you will want to change that reference to something you don't mind seeing in the folders list.

In the account in question, under the drafts & templates section of the "copies & folders" section I changed both templates and drafts to "keep messages in 'Local Folders'."

I then proceeded to exit out of Thunderbird, then deleted the files in question, then opened up Thunderbird again and they were gone. I then click on that account's Inbox file and they appear again as it logs in.

Then it is entirely possible you cannot permanently remove them once they have been created. If you really want them gone, you will need to create a new profile and migrate everything else (except the Templates folder(s)) into the new profile from the old. (On the other hand, creating a new profile and migrating all of your settings is a pretty stiff price to pay just to get rid of a folder...)

Do the new profile this way so that you don't move the problem in with the data:

To make this easier, you need to set Windows to "View hidden files and folders" and to not "Hide extensions for known file types". See this for easy instructions for how to do this: http://spywarewarrior.com/viewtopic.php?t=272 Use the instructions for XP if you're using Vista. They are the same.

Close Thunderbird and open the profile manager. http://kb.mozillazine.org/Profile_managerCreate your new profile, naming it something other than "default", and setup your accounts. Make sure it's working including for sending and receiving mail.

To install a Thunderbird extension do the following:Right click the download link and choose "Save Link As...". Then open Thunderbird, in Thunderbird go to Tools->Extensions->Install (Tools>Addons>Extensions in version 2.0). Find the just downloaded .xpi file and select it. The installation will now begin. You will need to close and reopen Thunderbird to complete the install.

When it's installed, first select the folder you want to import into and then go to Tools>Import/Export in Mbox/eml format and under it, Import Mbox File. In the next screen you will get a choice to either import a selected file or to select a directory. Select the third option and when you get to the Windows file navigation window, find your OLD profile under C:\Documents and Settings\*user name*\Application Data\Thunderbird\Profiles\*random string.profile name*\Mail and then select each account folder one at a time. This means that you will need to go through the Tools menu once for each account. The messages will be in a new folder named for the original with three numbers, ex: Inbox123, which you can then move the messages out of and sort as you want.

For your address books, install the MoreCols ForAddressBook extension. When it's installed you will have some new menu items under Tools in the address book manager. First open the manager with Tools>Address Book. Now go to it's Tools and find Actions for addressbook. Under it, select Import addressbook from mab file. It will ask you to create a new address book by naming it. Do so. Then, in the file navigation window that opens, find your old profile and look for the files with the .mab extension. Your personal address book is abook.mab and the collected is history.mab. You may have others that you either imported from another program or created yourself. You will need to do them one at a time. Once in, you can drag and drop the addresses from the imported books into your new Personal/Collected address book.

If you have any filters set in your accounts, the files you want to copy is msgFilterRules.dat This goes in the Mail/*account* folder. For Junk controls training, the file is training.dat and it is kept in the top level of the profile folder.

Well I created a new account, and then when I logged in all of the folders appeared at sign-in, I didn't have to do anything. And I managed to delete all of the folders I didn't want (i.e. templates) except the drafts folder....

Whenever I try to delete it in Thunderbird (when I got rid of the templates folder, I put it in the trash, then deleted the file and it stayed deleted. I was trying to copy that) it says:"AlertThe current command did not succeed. The mail server responded. Command Argument Error. 11."